[adegenet-commits] r372 - pkg/R

[noreply at r-forge.r-project.org]

Author: jombart
Date: 2009-06-05 14:42:40 +0200 (Fri, 05 Jun 2009)
New Revision: 372

Modified:
   pkg/R/haploSim.R
Log:
optimize.seqTrack.haploSim is complete.
Have to test all that now


Modified: pkg/R/haploSim.R
===================================================================
--- pkg/R/haploSim.R	2009-06-05 12:37:41 UTC (rev 371)
+++ pkg/R/haploSim.R	2009-06-05 12:42:40 UTC (rev 372)
@@ -378,15 +378,21 @@
 ## optimize.seqTrack.haploSim
 ##############################
 optimize.seqTrack.haploSim <- function(x, thres=0.2, optim=c("min","max"),
-                              prox.mat=NULL, nstep=10, step.size=1e3, mu0, seq.length,
-                              rMissDate=.rUnifTimeSeq, ...){
+                              prox.mat=NULL, nstep=10, step.size=1e3, rMissDate=.rUnifTimeSeq, ...){
 
     x <- dist.dna(x$seq, model="raw")
     seq.names <- labels(x)
     seq.dates <- as.POSIXct(sim)
     seq.length <- ncol(x$seq)
+    prevCall <- as.list(x$call)
+    if(is.null(prevCall$mu)){
+        mu0 <- 0.0001
+    } else {
+        mu0 <- prevCall$mu
+    }
 
-    res <- optimize.seqTrack.default(x, seq.names, seq.dates, thres=0.2, optim=c("min","max"),
-                              prox.mat=NULL, nstep=10, step.size=1e3, mu0, seq.length,
-                              rMissDate=.rUnifTimeSeq, ...)
+    res <- optimize.seqTrack.default(x=x, seq.names=seq.names, seq.dates=seq.dates,
+                                     thres=thres, optim=optim, prox.mat=prox.mat,
+                                     nstep=nstep, step.size=step.size, mu0=mu0,
+                                     seq.length=seq.length, rMissDate=rMissDate, ...)
 }